Cut out everything within a volume. Is it possible?
I have no such a big terrain here ... but this should work (with blender 2.8 at least...I don't know whether older versions will work).

Create the cylinder and position it at the correct place.

Select a mesh on the terrain inside the cylinder.
Add a boolean modifier and set it to intersect. Check the result.
If ok select everything and deselect the cylinder then.
Select the mesh from before.
Copy the boolean modifier with "copy selected modifier" to all the meshes.
deselect everything. Select the mesh from the start. 
Press ALT and then APPLY of the boolean modifier.
Make a backup of your blender file before :)